Arc Hydro tools simply convert the polyline to a raster with a value. The value can be very big. You can make the value a little more than you need to "burn" a stream into the embankment. Then, Arc Hydro subtracts the polyline value from the dem. The fill sinks function fills in the stream to allow the flow direction to go downstream.
You can do this without Arc Hydro. Draw a "stream" polyline through the embankment with the ends of the polyline where the low points are in the stream up and down stream of the embankment. Convert the stream to a raster with a high value, high enough the go below the embankment. (You may need to create a field in the polyline table for this value). Then, with with raster math, subtract your stream raster from the dem. After this, you use the resulting dem with the fill function and move on from there like you did before.
Arc Hydro will make the "burned stream" more than one cell wide. You may need to do that, though I'd try doing it with whatever results the polyline to raster conversion give you. Seem like it should work.